AB-Bind: Antibody binding mutational database for computational affinity predictions

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

(2015) Shane Ó Conchúir et al.   PLoS One

Biopharmaceutical benchmarks 2014

(2014) Gary Walsh   NATURE BIOTECHNOLOGY

A minimal model of protein-protein binding affinities

(2014) Joël Janin   PROTEIN SCIENCE

Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction

(2014) Kai Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins

(2014) Joe DeBartolo et al.   PLoS Computational Biology

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

(2013) Lingle Wang et al.   Journal of Chemical Theory and Computation

Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes

(2013) Hege Beard et al.   PLoS One

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

pH-selective mutagenesis of protein-protein interfaces:In silicodesign of therapeutic antibodies with prolonged half-life

(2013) Velin Z. Spassov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Antibody Therapeutics in Cancer

(2013) M. X. Sliwkowski et al.   SCIENCE

Toward aggregation-resistant antibodies by design

(2013) Christine C. Lee et al.   TRENDS IN BIOTECHNOLOGY

Antigen–antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures

(2012) Thiruvarangan Ramaraj et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

(2012) Iain H. Moal et al.   BIOINFORMATICS

Engineering Protein Therapeutics: Predictive Performances of a Structure-Based Virtual Affinity Maturation Protocol

(2012) Michael Oberlin et al.   Journal of Chemical Information and Modeling

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

(2012) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Predictive Bcl-2 Family Binding Models Rooted in Experiment or Structure

(2012) Joe DeBartolo et al.   JOURNAL OF MOLECULAR BIOLOGY

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

(2011) Mariana Babor et al.   PROTEIN SCIENCE

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

Design of next-generation protein therapeutics

(2010) Justin Caravella et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

(2010) Emmanuel D. Levy   JOURNAL OF MOLECULAR BIOLOGY

Transient Protein-Protein Interactions: Structural, Functional, and Network Properties

(2010) James R. Perkins et al.   STRUCTURE

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

(2009) Nurcan Tuncbag et al.   BIOINFORMATICS

Improving the species cross-reactivity of an antibody using computational design

(2009) Christopher J. Farady et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Testing Assumptions and Hypotheses for Rescoring Success in Protein−Ligand Docking

(2009) Noel M. O’Boyle et al.   Journal of Chemical Information and Modeling

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A feature-based approach to modeling protein–protein interaction hot spots

(2009) Kyu-il Cho et al.   NUCLEIC ACIDS RESEARCH

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design

(2008) Elisabeth L. Humphris et al.   STRUCTURE

Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm

(2008) Ignacio E. Sánchez et al.   PLoS Computational Biology

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE